Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression

Rajan, Arvind Arul Nambi; Montpetit, Ben

doi:10.1007/s00018-020-03680-y

Cited by 21 publications

(16 citation statements)

References 94 publications

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“…The nucleoporin Gle1 with the small molecule inositol hexakisphosphate (InsP 6 ) has been shown to synergistically activate Dbp5 ATPase activity at low RNA concentrations (Weirich, Erzberger et al 2006, Montpetit, Thomsen et al 2011). These findings have led to a model of spatially regulated Dbp5 activity to promote mRNA-protein complex remodeling at the cytoplasmic face of an NPC where Gle1 is localized, resulting in directional mRNA export (Hodge, Colot et al 1999, Strahm, Fahrenkrog et al 1999, Alcazar-Roman, Tran et al 2006, Weirich, Erzberger et al 2006, Dossani, Weirich et al 2009, Hodge, Tran et al 2011, Montpetit, Thomsen et al 2011, Noble, Tran et al 2011, Adams, Mason et al 2017, Wong, Gray et al 2018, Arul Nambi Rajan and Montpetit 2021). In the context of tRNA, addition of Gle1/InsP 6 maximally stimulated Dbp5 (1.03 +/- 0.04 ATP/s) to a level like that of ssRNA (1.11 +/- 0.07) (Figure 5B).…”

Section: Resultsmentioning

confidence: 99%

“…Here, a combination of in vivo and in vitro data provide evidence that (1) Dbp5 and Gle1 have functions independent of Los1 in tRNA export; (2) Dbp5 can bind tRNA directly in vitro and does so in a manner that does not require Los1, Msn5, and Mex67 in vivo; and (3) the Dbp5 ATPase cycle is uniquely modulated by Gle1 in the presence of structured RNA (e.g. tRNA or dsRNA) in vitro and the ATPase cycle supports tRNA export in vivo.DEAD-box proteins (including Dbp5) broadly interact with RNA via the phosphate backbone(Andersen, Ballut et al 2006, Andersen, Ballut et al 2006, Linder 2006, Sengoku, Nureki et al 2006, Arul Nambi Rajan and Montpetit 2021. The observed Dbp5-tRNA interaction is nucleotide dependent, supporting a specificity to the observed binding (Figure4A/B).…”

mentioning

confidence: 84%

“…Alcazar-Roman, Tran et al 2006, Weirich, Erzberger et al 2006, Dossani, Weirich et al 2009, Adams, Mason et al 2017, Wong, Gray et al 2018, Arul Nambi Rajan and Montpetit 2021). In the context of tRNA, addition of Gle1/InsP6 maximally stimulated Dbp5 (1.03 +/-0.04 ATP/s) to a level like that of ssRNA (1.11 +/-0.07) (Figure 5B).…”

Section: Arvind Arul Nambi Rajan 13mentioning

confidence: 99%

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Gle1 is required for tRNA to stimulate Dbp5 ATPase activityin vitroand to promote Dbp5 mediated tRNA exportin vivo

Rajan

Asada

Montpetit

2023

Preprint

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Cells must maintain a pool of processed and charged transfer RNAs (tRNA) to sustain translation capacity and efficiency. Numerous parallel pathways support the processing and directional movement of tRNA in and out of the nucleus to meet this cellular demand. Recently, several proteins known to control messenger RNA (mRNA) transport were implicated in tRNA export. The DEAD-box Protein 5, Dbp5, is one such example. In this study, genetic and molecular evidence demonstrates that Dbp5 functions parallel to the canonical tRNA export factor Los1. In vivo co-immunoprecipitation data further shows Dbp5 is recruited to tRNA independent of Los1, Msn5 (another tRNA export factor), or Mex67 (mRNA export adaptor), which contrasts with Dbp5 recruitment to mRNA that is abolished upon loss of Mex67 function. However, as with mRNA export, overexpression of Dbp5 dominant-negative mutants indicates a functional ATPase cycle and that binding of Dbp5 to Gle1 is required by Dbp5 to direct tRNA export. Biochemical characterization of the Dbp5 catalytic cycle demonstrates the direct interaction of Dbp5 with tRNA (or double stranded RNA) does not activate Dbp5 ATPase activity, rather tRNA acts synergistically with Gle1 to fully activate Dbp5. These data suggest a model where Dbp5 directly binds tRNA to mediate export, which is spatially regulated via Dbp5 ATPase activation at nuclear pore complexes by Gle1.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 84%

Section: Arvind Arul Nambi Rajan 13mentioning

confidence: 99%

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Gle1 is required for tRNA to stimulate Dbp5 ATPase activityin vitroand to promote Dbp5 mediated tRNA exportin vivo

Rajan

Asada

Montpetit

2023

Preprint

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“…During mRNA export, Dbp5 triggers remodelling of mRNAs emerging into the cytoplasm in the final export steps. Yeast Dbp5 is regulated by Gle1, an interaction stabilised by inositol-hexakisphosphate (IP 6 ), which catalyses the release of RNA-binding proteins to ensure directional transport from the nucleus [ 117 , 118 ]. However, in humans IP 6 binding may be dispensable [ 119 ], suggesting diverse mechanisms.…”

Section: Cytoplasmic Filaments and Mrna Exportmentioning

confidence: 99%

Evolution and diversification of the nuclear pore complex

Макаров

Padilla-Mejía

Field

2021

Biochemical Society Transactions

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The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.

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“…Rather, an ATP-dependent RNA helicase, DDX19 in mammals (Dpb5 in yeast), together with additional factors remodels and releases the mRNPs after export into the cytoplasm 8,9 .…”

Section: Introductionmentioning

confidence: 99%

Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time

Ruland

Krueger

Doerner

et al. 2021

Preprint

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Ribosomal subunit biogenesis within mammalian cells initiates in the nucleolus with the assembly of a 90S precursor particle, which is subsequently split into the pre-40S and pre-60S subunits. During further processing steps, pre-ribosomal subunits are loaded with export receptors, which enables their passage through the pore complexes (NPCs) into the cytoplasm. Here export factors are released and both subunits can form a mature ribosome. Ribosomal biogenesis has been studied in great detail by biochemical, genetic and electron microscopic approaches, however, until now live cell data on the in vivo kinetics are still missing. We analysed export kinetics of the large ribosomal subunit (pre-60S particle) through single NPCs in living human cells. To assess the in vivo dynamics of this process, we established a stable cell line co-expressing Halo-tagged eIF6 and GFP-fused NTF2 to simultaneously label ribosomal 60S subunits (eIF6) and NPCs (NTF2). By combining single molecule tracking and super resolution confocal microscopy in a highly customized microscopic setup, we visualized the dynamics of single pre-60S particles during the interaction with and export through single NPCs. In this way we obtained unprecedented insights into this key cellular process. Our results revealed that for export events, maximum particle accumulation is found in the centre of the pore, while unsuccessful export terminates within the nuclear basket. The export process takes place with a single rate limiting step and an export dwell time of ~24 milliseconds. Only about 1/3 of attempted export events were successful. Given the molecular mass of the pre-60S particles our results show that the mass flux through a single NPC can reach up to ~125 MDa s-1 in vivo.

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Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression

Cited by 21 publications

References 94 publications

Gle1 is required for tRNA to stimulate Dbp5 ATPase activityin vitroand to promote Dbp5 mediated tRNA exportin vivo

Gle1 is required for tRNA to stimulate Dbp5 ATPase activityin vitroand to promote Dbp5 mediated tRNA exportin vivo

Evolution and diversification of the nuclear pore complex

Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time

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